Setup

FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
1_non_mutant_Q96_K97del_6mth_10_03_2016_S1_fem_R1.fq.gz 45,225,393 0 35-150 45
1-MORGAN-6P-PN1_S2_R1_001.fq.gz 26,290,224 0 35-76 44
10_Ps2Ex3M1_WT_6month_07_07_2016_F3_86_Fem_R1.fq.gz 32,598,508 0 35-150 46
11__-_5_R1.fq.gz 21,272,369 0 35-76 45
11_Ps2Ex3M1_WT_6month_07_07_2016_F3_88_Fem_R1.fq.gz 34,573,446 0 35-150 47
12__-_4_R1.fq.gz 22,070,458 0 35-76 45
12_9W_1.fq.gz 51,361,917 0 35-150 44
12_Ps2Ex3M1_WT_6month_07_07_2016_F3_95_Fem_R1.fq.gz 3.2e+07 0 35-150 46
13__-_3_R1.fq.gz 1.7e+07 0 35-76 45
14__-_2_R1.fq.gz 24,266,600 0 35-76 45
15__-_1_R1.fq.gz 25,643,654 0 35-76 45
2_non_mutant_Q96_K97del_6mth_10_03_2016_S2_fem_R1.fq.gz 39,097,924 0 35-150 44
2-MORGAN-6P-PN2_S5_R1_001.fq.gz 45,232,784 0 35-76 44
3_13W_1.fq.gz 42,022,566 0 35-150 43
3_non_mutant_Q96_K97del_6mth_10_03_2016_S3_fem_R1.fq.gz 42,756,149 0 35-150 44
3-MORGAN-6P-PN3_S10_R1_001.fq.gz 29,274,876 0 35-76 44
4_14W_1.fq.gz 46,784,129 0 35-150 43
4_non_mutant_K97Gfs_6mth_10_03_2016_S1_fem_R1.fq.gz 46,346,616 0 35-150 43
4-MORGAN-6P-PN4_S8_R1_001.fq.gz 32,027,574 0 35-76 43
5_non_mutant_K97Gfs_6mth_10_03_2016_S2_fem_R1.fq.gz 38,963,892 0 35-101 43
6_16W_1.fq.gz 63,383,444 0 35-150 44
6_non_mutant_K97Gfs_6mth_10_03_2016_S3_fem_R1.fq.gz 83,022,890 0 35-150 44
8_19W_1.fq.gz 30,142,041 0 35-150 43
9_1W_1.fq.gz 21,154,240 0 35-150 43
9_Ps2Ex3M1_WT_6month_07_07_2016_F3_79_Fem_R1.fq.gz 27,960,314 0 35-150 47
W1_ss.fq.gz 46,324,895 0 35-150 43
W2_ss.fq.gz 44,093,591 0 35-150 44
W3_ss.fq.gz 45,456,094 0 35-150 43
W4_ss.fq.gz 53,914,220 0 35-150 43
W5_ss.fq.gz 41,470,209 0 35-150 43

Read Totals

Library Sizes ranged between 17,003,150 and 83,022,890 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Genome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Genome

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## Overrepresented_sequences missing from 1-MORGAN-6P-PN1_S2_R1_001.fq.gz
## Overrepresented_sequences missing from 11__-_5_R1.fq.gz
## Overrepresented_sequences missing from 12__-_4_R1.fq.gz
## Overrepresented_sequences missing from 12_9W_1.fq.gz
## Overrepresented_sequences missing from 13__-_3_R1.fq.gz
## Overrepresented_sequences missing from 14__-_2_R1.fq.gz
## Overrepresented_sequences missing from 15__-_1_R1.fq.gz
## Overrepresented_sequences missing from 2-MORGAN-6P-PN2_S5_R1_001.fq.gz
## Overrepresented_sequences missing from 3_13W_1.fq.gz
## Overrepresented_sequences missing from 3-MORGAN-6P-PN3_S10_R1_001.fq.gz
## Overrepresented_sequences missing from 4_14W_1.fq.gz
## Overrepresented_sequences missing from 4-MORGAN-6P-PN4_S8_R1_001.fq.gz
## Overrepresented_sequences missing from 6_16W_1.fq.gz
## Overrepresented_sequences missing from 8_19W_1.fq.gz
## Overrepresented_sequences missing from 9_1W_1.fq.gz
## Overrepresented_sequences missing from W1_ss.fq.gz
## Overrepresented_sequences missing from W2_ss.fq.gz
## Overrepresented_sequences missing from W3_ss.fq.gz
## Overrepresented_sequences missing from W4_ss.fq.gz
## Overrepresented_sequences missing from W5_ss.fq.gz
Summary of Overrepresented Sequences in all files. A maximum of 30 seqences are shown.
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
CCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCC 1,915,608 10 0.166% 0.65% No Hit
CGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCC 1,673,850 6 0.145% 0.66% No Hit
GTGGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGC 1,421,432 4 0.123% 1.66% No Hit
GGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATC 1,195,842 4 0.104% 1.08% No Hit
CTGAAGTCTTGGAGCTCGACTTCCCTACGTTTCGCCTACAAATGTTGCCT 866,936 6 0.075% 0.35% No Hit
GGGGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTG 719,598 4 0.062% 1.03% No Hit
GTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATCT 660,825 4 0.057% 0.57% No Hit
GGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCAT 645,351 4 0.056% 0.76% No Hit
CTTAGACGACCTGGTAGTCCAAGGCTCCCCCAGGAGCACCATATCGATAC 501,473 7 0.044% 0.26% No Hit
CCTCCTTCAAGTATTGTTTCATGTTACATTTTCGTATATTCTGGGGTAGA 462,364 4 0.040% 0.57% No Hit
CTCCTGAAAAGGTTGTATCCTTTGTTAAAGGGGCTGTACCCTCTTTAACT 438,172 3 0.038% 0.69% No Hit
GCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCCA 418,110 6 0.036% 0.16% No Hit
CGGGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGG 412,467 4 0.036% 0.73% No Hit
GGGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTT 406,142 3 0.035% 0.59% No Hit
GTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCCACTA 364,611 6 0.032% 0.14% No Hit
GGGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTGC 358,921 4 0.031% 0.44% No Hit
CGGGTCGGGTGGGTAGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGG 342,333 4 0.030% 0.56% No Hit
CCCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATC 315,738 4 0.027% 0.39% No Hit
CTCCGACCTGGGCCGGTTCACCCCTCCTTAGACGACCTGGTAGTCCAAGG 238,609 4 0.021% 0.12% No Hit
GGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTTA 219,458 3 0.019% 0.37% No Hit
ATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCCCACTACT 190,314 3 0.017% 0.12% No Hit
GGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTGCC 182,193 4 0.016% 0.21% No Hit
AGCTGGGGAGATCCGCGAGAAGGGCCCGGCGCACGTCCAGAGTCGCCGCC 174,069 3 0.015% 0.23% No Hit
GGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGGAC 171,124 3 0.015% 0.25% No Hit
GTCCCCCACTACCAGAAATTATGCAGTCGAGATTCCCACATTTGGGGAAT 160,169 3 0.014% 0.19% No Hit
GGCCCGGCGCACGTCCAGAGTCGCCGCCGCGCACCGCAGCGCATCCCCCC 155,419 2 0.013% 0.35% No Hit
GTCTGAAGTCTTGGAGCTCGACTTCCCTACGTTTCGCCTACAAATGTTGC 155,346 3 0.013% 0.23% No Hit
GCCCACTACGACAACGTGTTTTGTAAATTATGATCTTTATTCTCCTGAAA 152,742 2 0.013% 0.24% No Hit
GCTCGGGTGTCTACATCCATTCCTACAGTGAATATGTGATGGGCTCATAC 142,619 3 0.012% 0.20% No Hit
TGGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCA 133,783 3 0.012% 0.19% No Hit

Adapter Content

Universal Adapter Content

Kmer Content

## Kmer_Content missing from 1_non_mutant_Q96_K97del_6mth_10_03_2016_S1_fem_R1.fq.gz
## Kmer_Content missing from 1-MORGAN-6P-PN1_S2_R1_001.fq.gz
## Kmer_Content missing from 10_Ps2Ex3M1_WT_6month_07_07_2016_F3_86_Fem_R1.fq.gz
## Kmer_Content missing from 11__-_5_R1.fq.gz
## Kmer_Content missing from 11_Ps2Ex3M1_WT_6month_07_07_2016_F3_88_Fem_R1.fq.gz
## Kmer_Content missing from 12__-_4_R1.fq.gz
## Kmer_Content missing from 12_9W_1.fq.gz
## Kmer_Content missing from 12_Ps2Ex3M1_WT_6month_07_07_2016_F3_95_Fem_R1.fq.gz
## Kmer_Content missing from 13__-_3_R1.fq.gz
## Kmer_Content missing from 14__-_2_R1.fq.gz
## Kmer_Content missing from 15__-_1_R1.fq.gz
## Kmer_Content missing from 2_non_mutant_Q96_K97del_6mth_10_03_2016_S2_fem_R1.fq.gz
## Kmer_Content missing from 2-MORGAN-6P-PN2_S5_R1_001.fq.gz
## Kmer_Content missing from 3_13W_1.fq.gz
## Kmer_Content missing from 3_non_mutant_Q96_K97del_6mth_10_03_2016_S3_fem_R1.fq.gz
## Kmer_Content missing from 3-MORGAN-6P-PN3_S10_R1_001.fq.gz
## Kmer_Content missing from 4_14W_1.fq.gz
## Kmer_Content missing from 4_non_mutant_K97Gfs_6mth_10_03_2016_S1_fem_R1.fq.gz
## Kmer_Content missing from 4-MORGAN-6P-PN4_S8_R1_001.fq.gz
## Kmer_Content missing from 5_non_mutant_K97Gfs_6mth_10_03_2016_S2_fem_R1.fq.gz
## Kmer_Content missing from 6_16W_1.fq.gz
## Kmer_Content missing from 6_non_mutant_K97Gfs_6mth_10_03_2016_S3_fem_R1.fq.gz
## Kmer_Content missing from 8_19W_1.fq.gz
## Kmer_Content missing from 9_1W_1.fq.gz
## Kmer_Content missing from 9_Ps2Ex3M1_WT_6month_07_07_2016_F3_79_Fem_R1.fq.gz
## Kmer_Content missing from W1_ss.fq.gz
## Kmer_Content missing from W2_ss.fq.gz
## Kmer_Content missing from W3_ss.fq.gz
## Kmer_Content missing from W4_ss.fq.gz
## Kmer_Content missing from W5_ss.fq.gz
## No Kmers were detected by FastQC